Since I came out in school half a year ago and I have used the male toilet since then, I can only advice you to give it a try when you feel like that.
I got the chance to get a key to a different toilet not used by anyone except of during exams, but I refused to take it. At first I feared the guys in my year were throwing me out of the room, but they never did that at all. There were some glances of the boys in my year or of others who know me, but I usually pass for all the boys who don't know me as long as I keep my mouth shut, so it works very well, better than I expected it to be.
I still prefer going there after the breaks and during lessons, but I go there during my breaks now as well, even my year-headteacher admired me for being so confident when he once saw me really going there.
I believe that it is some kind of respect you gain and people take you more seriously when you do that after coming out. (I made the experience that some folks asked whether it was just a phase or something like that... -.-

)
And I have to agree with MrMann. You don't really care about who is with you in the bathroom as a male, the entire 'procedure' in there is so different from what happens in a females' bathroom... [At least in Germany]